HTSMultiQC-cleaning-report
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-10-23, 11:28 PDT
based on data in:
/mnt/analysis/cat_users/matt/rnaseq_example/01-HTS_Preproc
General Statistics
| Sample Name | M Input | M Output |
|---|---|---|
| NEB_Mixed-10-ng-1_1M_S383 | 1.00 | 0.41 |
| NEB_Mixed-10-ng-2_S384 | 1.00 | 0.41 |
| NEB_Mixed-10-ng-3_S385 | 1.00 | 0.41 |
HTStream
HTStream quality control and processing pipeline for High Throughput Sequencing data.URL: https://s4hts.github.io/HTStream
Processing Overview
Plots reduction of reads and basepairs across the preprocessing pipeline.
hts_Stats_1 Table
Basic statistics about the reads in a dataset.
initial stats
| Sample Name | % R1 Q30 | % R2 Q30 | GC Content | N Content |
|---|---|---|---|---|
| NEB_Mixed-10-ng-1_1M_S383 | 95.14% | 95.14% | 46.74% | 0.0016% |
| NEB_Mixed-10-ng-2_S384 | 95.05% | 95.05% | 46.63% | 0.0016% |
| NEB_Mixed-10-ng-3_S385 | 95.17% | 95.17% | 46.47% | 0.0016% |
hts_Stats_1 PE Read Length
Distribution of read lengths for each sample.
| Sample Name | R1 Read Lengths | R2 Read Lengths |
|---|---|---|
| NEB_Mixed-10-ng-1_1M_S383 | 151 | 151 |
| NEB_Mixed-10-ng-2_S384 | 151 | 151 |
| NEB_Mixed-10-ng-3_S385 | 151 | 151 |
hts_Stats_1 PE Base by Cycle
Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.
hts_Stats_1 PE Quality by Cycle
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
hts_SeqScreener_1
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
screen phix
hts_SeqScreener_2
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
count the number of rRNA reads
hts_SuperDeduper
A reference free duplicate read removal tool.
remove PCR duplicates
hts_Overlapper
Attempts to overlap paired end reads to produce the original fragment, trims adapters, and can correct sequencing errors.
trim adapters
hts_PolyATTrim
Attempts to trim poly-A and poly-T sequences from the end of reads.
remove polyAT tails
hts_NTrimmer
Trims reads to the longest subsequence that contains no N's.
remove any remaining N characters
hts_QWindowTrim
Uses a sliding window approach to remove the low quality ends of reads.
quality trim the ends of reads
hts_LengthFilter
Discards reads below a minimum length threshold.
remove reads < 50bp
hts_Stats_2 Table
Basic statistics about the reads in a dataset.
final stats
| Sample Name | % R1 Q30 | % R2 Q30 | % SE Q30 | GC Content | N Content |
|---|---|---|---|---|---|
| NEB_Mixed-10-ng-1_1M_S383 | 95.91% | 95.91% | 95.65% | 45.41% | 0.0000% |
| NEB_Mixed-10-ng-2_S384 | 95.83% | 95.83% | 95.79% | 45.40% | 0.0000% |
| NEB_Mixed-10-ng-3_S385 | 95.93% | 95.93% | 95.64% | 45.37% | 0.0000% |
hts_Stats_2 PE Read Length
Distribution of read lengths for each sample.
hts_Stats_2 PE Base by Cycle
Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.
hts_Stats_2 PE Quality by Cycle
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
hts_Stats_2 SE Read Length
Distribution of read lengths for each sample.
hts_Stats_2 SE Base by Cycle
Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.
hts_Stats_2 SE Quality by Cycle
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
